USP47 / Ubiquitin carboxyl-terminal hydrolase 47 · IHC design guide

Design Immunohistochemistry for USP47

Plan USP47 chromogenic IHC-P around its widespread cytoplasmic tissue staining (HPA tissue IHC). This guide covers fixation, tissue controls and scoring by cell type and staining intensity.

Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use

Immunohistochemistry protocol sheet for USP47 (IHC for USP47): expected localisation Cytoplasmic tissue staining (HPA tissue IHC), antibody M07648, validated IHC image, and IHC protocol steps — Printable **USP47** IHC protocol sheet — expected localisation Cytoplasmic tissue staining (HPA tissue IHC), antibody M07648, controls and protocol steps. Open the full USP47 IHC guide →

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USP47 Immunohistochemistry Experimental Design Guide

Expected localisation, validated protocols, controls and antibodies — the at-a-glance facts below, then the full design guide.

Must know before staining

	Expected localisation	Cytoplasmic tissue staining (HPA tissue IHC)
	Staining pattern	Widespread cytoplasmic staining across cell types (HPA tissue IHC)
	Antigen retrieval	Citrate pH 6 HIER, heat-mediated (datasheet M07648)
	Positive control ⓘ	Adrenal gland+4 more · see all
	Negative control ⓘ	None in HPA (detected in all 45 tissues); use no-primary + isotype controls

Important caveats

Reasons your staining may differ from the expected pattern.

	Fixation	Use formaldehyde-fixed paraffin sections (datasheet M07648 IHC-P). (selected-SKU IHC image M07648)
	Caveat	Intensity varies by cell type despite widespread staining (HPA tissue IHC)
	Regulation	No specific staining-linked regulation reported (UniProt)
	Isoform / epitope	4 isoforms; epitope coverage is unclear (UniProt)

Section 1

Recommended USP47 IHC & IF Protocols

The catalog antibody protocol uses citrate pH 6 retrieval (datasheet M07648). One published USP47 IHC protocol provides an artery tissue comparison (PMC9090392).

Recommended immunohistochemistry (IHC-P) protocol parameters
Sample	Formaldehyde-fixed, paraffin-embedded human skeletal muscle tissue (datasheet M07648)
Fixation	Image formalin-fixed; duration unreported (datasheet M07648); verify before use.
Sectioning	4–5 µm sections on charged slides (standard)
Deparaffinisation	Xylene, graded ethanol series to water (standard)
Antigen retrieval	Heat retrieval: Citrate pH 6 (datasheet M07648); 20 min, 95–100 °C (standard)
Peroxidase block	3% H2O2, 10 min, room temperature (standard)
Blocking	10% normal serum of the secondary host, 30 min, room temperature (standard)
Primary antibody	Rabbit anti-USP47, 1:25 (datasheet M07648)
Primary incubation	1 hours at 37°C (datasheet M07648)
Detection	HRP-polymer secondary, DAB chromogen 5–10 min (standard)
Counterstain	Hematoxylin, blue, dehydrate and mount (standard)
Expected result	USP47-positive staining in glandular cells of adrenal gland (HPA tissue IHC: High). HPA tissue profile: Ubiquitous cytoplasmic expression. No signal in the no-primary control.

💡Decision noteStart with citrate pH 6 retrieval for the catalog antibody (datasheet M07648); the published artery protocol used pH 8 (PMC9090392).

Section 2

What Is the Expected USP47 Staining Pattern?

USP47 is a cytoplasmic protein with no transmembrane segment (UniProt Q96K76). In paraffin-section IHC, expect cytoplasmic staining across many cell types, including strong staining in colon glandular cells and bronchial respiratory epithelial cells (HPA tissue IHC). HPA describes the tissue pattern as ubiquitous cytoplasmic expression, with Supported reliability and medium consistency between antibody staining and RNA expression (HPA tissue IHC).

What am I looking at on my slide?
Cytoplasmic chromogen in colon glandular cells or bronchial respiratory epithelial cells.	This fits the reported compartment and High staining in those cells (HPA tissue IHC). Compare signal with a no-primary control before scoring it as specific (general IHC practice).
Predominantly nuclear, membranous, or extracellular staining with little cytoplasmic signal.	That distribution does not fit the reported cytoplasmic pattern or absence of a transmembrane segment (HPA tissue IHC; UniProt Q96K76). Check controls and detection conditions; compartment mismatch alone cannot identify the artefact (general IHC practice).
Strong staining confined to an unexpected cell population while reported high-staining cells remain faint.	Question antibody specificity or endogenous detection activity (general IHC practice). USP47 staining is broadly reported, so an unlisted cell type is not automatically negative; HPA lists low, rather than absent, staining in several populations (HPA tissue IHC).
Diffuse chromogen across cells, stroma, and blank slide areas.	A pattern without cellular definition is difficult to assign to USP47. Compare the no-primary control, blocking, and chromogen development before interpreting it (general IHC practice); HPA reports a cellular cytoplasmic pattern (HPA tissue IHC).
No visible signal in a section containing colon glandular cells expected to stain strongly.	This conflicts with the reported High signal for those cells (HPA tissue IHC). First assess section and detection controls, then review the antibody's validated IHC conditions (general IHC practice).

💡Expected USP47 appearanceCall a result consistent with USP47 when chromogen is chiefly cytoplasmic and strong in reported high-staining cells such as colon glandular cells; isolated nuclear, membranous, or acellular signal needs control-based review (HPA tissue IHC; UniProt Q96K76; general IHC practice).

How each factor affects the staining
Tissue and cell selection	HPA reports High staining in glandular cells of adrenal gland, breast, cervix, colon, and duodenum, plus bronchial respiratory epithelial and caudate and cortical neuronal cells (HPA tissue IHC). These provide observed patterns for comparison, not guaranteed positive controls for every antibody (general IHC practice).
Low-staining populations	Ovarian stromal cells, splenic red-pulp cells, and bone-marrow hematopoietic cells are listed as Low, not negative (HPA tissue IHC). Faint staining there can be consistent with the record; absence there is weaker evidence of assay failure than absence in reported high-staining cells.
IF/ICC: should filaments appear on the IHC slide?	HPA ICC-IF places USP47 mainly at intermediate filaments and additionally at vesicles (HPA subcellular ICC-IF). Those finer patterns need not be resolved by chromogenic paraffin IHC; judge its broader cytoplasmic distribution against tissue IHC (HPA tissue IHC; general IHC practice).
Antibody evidence	HPA029286 and HPA029289 are both Supported for IHC; only HPA029286 is listed as Approved for ICC (HPA antibodies). These grades describe the listed antibodies and applications, so they do not validate a different catalog antibody or transfer an ICC pattern to IHC.
Isoforms and epitope coverage	UniProt lists 4 USP47 isoforms (UniProt Q96K76). Without the IHC antibody's epitope and isoform coverage, the record cannot predict which isoforms contribute to staining; resolve that question from antibody documentation rather than the slide pattern alone.
Processing and modifications	UniProt reports no signal peptide or propeptide and lists acetylation and phosphorylation sites (UniProt Q96K76). These annotations do not establish staining intensity, antigen-retrieval needs, or fixation sensitivity for the IHC antibody; target-specific effects are unreported here.

Why is my staining missing, weak or wrong?
Situation	Likely cause	Next action
No cytoplasmic signal in reported high-staining cells.	Section, primary-antibody, or detection failure is possible (general IHC practice); the absent result differs from reported High staining (HPA tissue IHC).	Confirm tissue identity and cellular preservation, run a suitable positive control, and check the catalog antibody's IHC-P instructions and detection reagents (general IHC practice).
Strong signal is mainly nuclear or on cell borders.	The compartment conflicts with cytoplasmic USP47 and its lack of a transmembrane segment (HPA tissue IHC; UniProt Q96K76); the pattern alone does not prove cross-reactivity.	Compare no-primary and positive-control sections, then reassess antibody specificity and staining conditions before assigning the signal to USP47 (general IHC practice).
Diffuse background obscures cell boundaries.	Nonspecific reagent binding or excessive chromogen development may obscure cellular staining (general IHC practice). HPA's reported tissue pattern is cytoplasmic (HPA tissue IHC).	Inspect the no-primary control; review blocking, washing, primary concentration, and development time using the assay instructions (general IHC practice).
Brown signal persists in the no-primary control.	Endogenous peroxidase activity or another detection-system background source is possible in chromogenic IHC (general IHC practice).	Review the peroxidase-quenching step and detection reagents, then repeat the control before interpreting cell-type staining (general IHC practice).
An unlisted cell type stains more strongly than an HPA low-staining population.	HPA describes broad cytoplasmic expression and lists some populations as Low; it supplies no negative tissue category here (HPA tissue IHC).	Check compartment, tissue identity, and controls. Do not call the unlisted population cross-reactive solely because it is absent from HPA's high-staining examples (HPA tissue IHC; general IHC practice).
IF/ICC shows filament-like signal, but paraffin IHC looks broadly cytoplasmic.	HPA reports intermediate-filament and vesicle localization by ICC-IF, alongside ubiquitous cytoplasmic tissue IHC (HPA subcellular ICC-IF; HPA tissue IHC).	Interpret each assay at its own resolution; use the tissue IHC pattern and IHC controls for the chromogenic section (HPA tissue IHC; general IHC practice).

Source: UniProt Q96K76 Human Protein Atlas tissue Human Protein Atlas subcellular

Experiment evidence

IHC & IF images showing USP47 staining

M07648 staining USP47 in human skeletal muscle tissue sections by Immunohistochemistry (IHC-P -paraformaldehyde-fixed, paraffin-embedded sections). Tissue was fixed with formaldehyde and blocked with 3% BSA for 0. 5 hour at room temperature; antigen retrieval was by heat mediation with a citrate buffer (pH6). Samples were incubated with primary antibody (1/25) for 1 hours at 37°C. A undiluted biotinylated goat polyvalent antibody was used as the secondary antibody.

M07648 · IHCM07648 staining USP47 in human skeletal muscle tissue sections by Immunohistochemistry (IHC-P -paraformaldehyde-fixed, paraffin-embedded sec

HPA · Cerebral cortexHuman Protein Atlas IHC, Cerebral cortex. Source: https://www.proteinatlas.org/ENSG00000170242-USP47/tissue/cerebral+cortex#imid_7935466

HPA · HippocampusHuman Protein Atlas IHC, Hippocampus. Source: https://www.proteinatlas.org/ENSG00000170242-USP47/tissue/hippocampal+formation#imid_7935467

HPA · ColonHuman Protein Atlas IHC, Colon. Source: https://www.proteinatlas.org/ENSG00000170242-USP47/tissue/colon#imid_7934082

HPA · LiverHuman Protein Atlas IHC, Liver. Source: https://www.proteinatlas.org/ENSG00000170242-USP47/tissue/liver#imid_7934083

HPA · ICC-IF A-431Human Protein Atlas immunofluorescence, A-431, antibody HPA029286; green = USP47, blue = nucleus, red = microtubules.

← swipe / scroll for more images →

Real IHC / IF data behind the staining-pattern expectations in this section.

Sample controls for USP47 IHC & IF

🧪Run breast tissue first and expect staining in its glandular cells (HPA: High in breast glandular cells). HPA detects USP47 in all 45 scored tissues, so there is no HPA-supported negative tissue; use no-primary and isotype controls, and treat cells on the positive slide that lack convincing signal as background comparators rather than validated negative cells (HPA: no negative rows; USP47 detected in all 45 scored tissues).

Positive control tissue: Adrenal gland (Glandular cells, HPA High)

Negative control tissue: None in HPA: USP47 is detected in all 45 scored tissues. Use a no-primary (secondary-only) and an isotype control instead.

ICC-IF cell lines (HPA subcellular resource): HPA ICC-IF images show USP47 in A-431, SiHa, U2OS, with annotated localisation: Intermediate filaments (approved) (HPA subcellular).

Technical controls: Include a no-primary, secondary-only section; a control IgG matched to the primary antibody’s host species and isotype, or host-matched nonimmune IgG for a polyclonal primary; and USP47-knockout material as a biological negative. Block endogenous peroxidase for chromogenic detection and check endogenous biotin if using the caption’s biotinylated secondary antibody (M07648 tissue-IHC caption: biotinylated secondary).

⚠️Feasibility: The selected M07648 paraffin-section caption reports heat-mediated citrate retrieval at pH 6, but establishes neither a USP47-specific retrieval requirement nor a fixation window; the fixative is unreported in the supplied caption metadata (M07648 tissue-IHC caption). The supplied evidence does not show whether frozen sections or IF/ICC are easier; HPA does provide ICC-IF images for USP47 (HPA: subcellular record). In breast sections, assess glandular-cell staining against background and endogenous peroxidase or biotin signal when using chromogenic, biotin-based detection (HPA: High in breast glandular cells; M07648 tissue-IHC caption: biotinylated secondary).

HPA tissue IHC evidence for USP47

Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Supported — Medium consistency between antibody staining and RNA expression data.). Rows are taken directly from the HPA tissue chart — click any row's HPA link to view the source.

Positive expression · recommended positive controls

Tissue	Cell type	Level	Evidence	Source
Adrenal gland	Glandular cells	High	Protein (IHC)	HPA →
Breast	Glandular cells	High	Protein (IHC)	HPA →
Bronchus	Respiratory epithelial cells	High	Protein (IHC)	HPA →
Caudate	Neuronal cells	High	Protein (IHC)	HPA →
Cerebral cortex	Neuronal cells	High	Protein (IHC)	HPA →

Undetected expression · recommended negative controls

Tissue	Cell type	Level	Evidence	Source
None in HPA: USP47 is detected in all 45 scored tissues. Use a no-primary (secondary-only) and an isotype control instead.

Section 3

Advanced USP47 IHC Tips

Troubleshoot USP47 staining in paraffin sections by checking retrieval, compartment, controls, and scoring before interpreting biological differences.

How should I optimize antigen retrieval when USP47 staining is weak?

Start with heat-mediated citrate retrieval at pH 6 for paraffin sections (datasheet M07648). Keep heating and cooling conditions identical across test sections, then compare signal in skeletal muscle with a no-primary control; the catalog image used this tissue and retrieval method (datasheet M07648; standard IHC practice). If signal remains weak, test a second retrieval condition on adjacent sections as a fallback, changing only that condition so its effect can be judged (standard IHC practice). Check whether any gain is cytoplasmic and cellular, since diffuse edge staining alone does not match the reported tissue profile (HPA: ubiquitous cytoplasmic expression; standard IHC practice).

Could fixation explain uneven USP47 staining across paraffin sections?

USP47-specific sensitivity to fixation is unknown; do not infer it from tissue staining patterns or protein features (evidence supplied here: no target-specific fixation comparison). Record fixative, fixation duration, tissue thickness, and time before fixation for each specimen, then compare sections processed together (standard IHC practice). If staining varies within a section, inspect poorly preserved regions and cut edges before changing the antibody dilution, because processing can alter antigen accessibility (standard IHC practice). Use an identically processed positive tissue section and a no-primary control to separate a run-wide staining problem from specimen variation (standard IHC practice).

Which staining compartment should I accept as USP47-positive?

Expect predominantly cytoplasmic staining in tissue IHC (UniProt Q96K76: cytoplasm; HPA: ubiquitous cytoplasmic expression). Score cellular cytoplasmic signal separately from nuclear or extracellular deposits, and inspect the same cell populations across matched sections (standard IHC practice). Intermediate-filament and vesicular patterns are reported in cell imaging, but a filament-like pattern is not required to call a tissue section positive (HPA subcellular: intermediate filaments and vesicles; HPA tissue IHC: cytoplasmic expression). If a nuclear-only pattern dominates, repeat staining with retrieval and no-primary controls before assigning it to USP47, because it conflicts with the supplied localisation evidence (UniProt Q96K76; HPA tissue IHC; standard IHC practice).

Can this antibody distinguish USP47 isoforms or modified epitopes in tissue?

Do not assign isoform identity from staining intensity alone: USP47 has 4 listed isoforms, while the supplied antibody evidence does not map its epitope (UniProt Q96K76; supplied M07648 evidence). The USP domain spans residues 188–564, and reported modifications include acetyllysine 122 and phosphoserines 832, 910, 933, and 1013 (UniProt Q96K76). Check an independently documented epitope sequence before predicting isoform coverage or modification sensitivity (standard IHC practice). For a disputed staining pattern, compare sections with an independently validated antibody recognizing a documented distinct epitope, while retaining the same cell-level scoring rules (standard IHC practice).

How can I assess USP47 by multiplex IF without misreading tissue background?

For multiplex IF, pair USP47 with a marker that identifies the expected cell population, such as a respiratory epithelial cell marker when examining bronchus (HPA: high USP47 staining in bronchial respiratory epithelial cells; standard IF practice). Choose fluorophores after imaging an unstained section in each channel, and place the weaker expected signal in a channel with lower tissue autofluorescence (standard IF practice). Because USP47 has no transmembrane segment and is reported in the cytoplasm, use controlled permeabilisation to reach an intracellular epitope, then compare permeabilised and untreated sections if epitope access is uncertain (UniProt Q96K76; standard IF practice). Report IF conditions separately from the catalog antibody’s chromogenic tissue protocol (datasheet M07648).

What should I adjust when USP47 staining appears diffusely brown?

Compare a no-primary section and a matched section with the primary antibody before changing conditions; brown deposits present without primary antibody indicate detection or tissue background (standard IHC practice). The catalog image used 3% BSA for 0.5 hour and primary antibody at 1:25 for 1 hour at 37°C (datasheet M07648). If background rises with primary antibody, titrate primary concentration and confirm adequate washing and blocking on adjacent sections (standard IHC practice). Include a peroxidase block for enzyme-based chromogenic detection, and judge retained signal by its cellular cytoplasmic distribution rather than uniform surface staining (standard IHC practice; HPA: ubiquitous cytoplasmic expression).

How should I score USP47 across sections with different cell mixtures? ⚠ ANSWER MARKED FOR VERIFICATION

Define the cell population and cytoplasmic compartment before scoring; USP47 tissue staining is reported as broadly cytoplasmic (HPA: ubiquitous cytoplasmic expression). For a defined population, report an H-score from percentage of cells at each intensity, alongside the percentage positive, using the same positivity threshold across sections (standard IHC practice). Normalize counts or positive area to the number of eligible cells or measured tissue area, such as cells per mm², and exclude folds and necrotic regions by a predefined rule (standard IHC practice). Keep acquisition, counterstain, and batch controls consistent; HPA rates tissue staining as Supported with medium agreement between staining and RNA expression (HPA tissue IHC; standard IHC practice).

How do I distinguish genuine USP47 staining from an artefact?

A credible positive is cellular and mainly cytoplasmic within an identifiable tissue cell population (UniProt Q96K76: cytoplasm; HPA: ubiquitous cytoplasmic expression). Compare morphology and a no-primary control: staining restricted to section edges, folds, necrosis, or areas with endogenous enzyme activity warrants investigation before scoring (standard IHC practice). Do not treat a nuclear-only or extracellular deposit pattern as confirmation of USP47 without independent validation, because the supplied localisation evidence favors cytoplasm (UniProt Q96K76; HPA tissue IHC). Interpret low signal cautiously in ovarian stroma, splenic red-pulp cells, and bone-marrow hematopoietic cells, which are listed as low rather than negative (HPA tissue IHC).

Boster reagents

Best USP47 / Ubiquitin carboxyl-terminal hydrolase 47 IHC Antibodies

Real IHC-P data cover human skeletal muscle paraffin sections with M07648 (M07648 image caption); the catalog supplies no IF/ICC image (catalog image payload).

Real IHC data

Anti-USP47 Antibody (Center)

Cat # M07648

View product →

M07648 is the sole card and shows USP47 staining in human skeletal muscle paraffin sections (M07648 image caption). Its caption reports formaldehyde fixation, citrate pH 6 retrieval, and a 1:25 primary dilution (M07648 image caption).

Which to pick: Choose M07648 for human tissue IHC-P: it is a rabbit polyclonal listed for human IHC-P, with paraffin-section staining documented in its own caption (catalog host, clonality, reactivity, and applications; M07648 image caption). No listed SKU has IF/ICC validation (catalog applications and IF image payload). No listed SKU has cross-species reactivity; M07648 is listed for human samples only (catalog reactivity).

Each figure is that product's own IHC / IF validation image from its datasheet.

References

UniProt Consortium. UniProt entry Q96K76 (UBP47_HUMAN, Ubiquitin carboxyl-terminal hydrolase 47).
Human Protein Atlas. USP47 tissue IHC expression (reliability: Supported).
Human Protein Atlas. USP47 subcellular location (ICC-IF): Mainly localized to the intermediate filaments. In addition localized to vesicles..
Human Protein Atlas. USP47 antibody validation summary (2 antibodies).
Ubiquitin-specific protease 47 is associated with vascular calcification in chronic kidney disease by regulating osteogenic transdifferentiation of vascular smooth muscle cells. Renal failure 2022 — PMC9090392.
USP47-Mediated Deubiquitination and Stabilization of TCEA3 Attenuates Pyroptosis and Apoptosis of Colorectal Cancer Cells Induced by Chemotherapeutic Doxorubicin. Frontiers in pharmacology 2021 — PMC8495243.
Targeting USP47 overcomes tyrosine kinase inhibitor resistance and eradicates leukemia stem/progenitor cells in chronic myelogenous leukemia. Nature communications 2021 — PMC7782553.
USP47 deubiquitylates Groucho/TLE to promote Wnt-β-catenin signaling. Science signaling 2023 — PMC10038201.
PubMed PMID:14702039 — UniProt-cited evidence.
PubMed PMID:16554811 — UniProt-cited evidence.
PubMed PMID:15489334 — UniProt-cited evidence.